A change in the goalkeeping department saw Sifiso Mlungwana come in for Mondli Mpoto, with Liam Jordan, McBeth Mahlangu and Lyle Foster also handed a start.
The Egyptians wasted no time to make their intentions known after the opening exchanges when Ahmed Yasser opened the scoring on 16 minutes before they doubled their lead just before the midway point to complete his brace.
It became worse for the visiting team a little later as Karim El Eraki went on to extend Egypt's lead, with David Notoane's side now having their work cut out to launch a way back.
Notoane kept the faith with the eleven from the first spell soon following the start of the second stanza amidst the fact that they trailed by a hefty score-line.
There was finally movement from the visitors' dugout inside the final quarter, as Luke Fleurs and Kgaogelo Sekgota came on for Bongani Sam and Jordan respectively.
More changes from the bench came as the clicked ticked in goalkeeper Lincoln Vyer, Keletso Makgalwa, Thabiso Monyane and Thendo Mukumela.
The Egyptians though managed the rest of the match to see out another win over their South African counterparts.